› 3fht

X-ray diffraction
2.2Å resolution

Crystal structure of human Dbp5 in complex with AMPPNP and RNA

Released:
DOI: 10.2210/pdb3fht/pdb
PDB entry 3fht coloured by chain, front view.
PDB entry 3fht coloured by chain, side view.
PDB entry 3fht coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner.
von Moeller H, Basquin C, Conti E
Nat Struct Mol Biol 16 247-54 (2009)
PMID: 19219046

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193967 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
ATP-dependent RNA helicase DDX19B Chains: A, B
Molecule details ›
Chains: A, B
Length: 412 amino acids
Theoretical weight: 46.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9UMR2 (Residues: 68-479; Coverage: 86%)
Gene names: DBP5, DDX19, DDX19B, TDBP
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand GOL 4 x GOL
Ligand ANP 2 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 41.6Å b: 79.66Å c: 124.54Å
α: 90° β: 90.02° γ: 90°
R-values:
R R work R free
0.171 0.168 0.225
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

45 review citations

From unwinding to clamping - the DEAD box RNA helicase family.
Linder et al. (2011)
44 more

10 mentions without citation

Building RNA-protein granules: insight from the germline.
Arkov et al. (2010)
9 more